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[sbml-svn] SF.net SVN: sbml:[15322] trunk/libsbml/dev/utilities
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From: <fbe...@us...> - 2012-01-26 20:36:23
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Revision: 15322
http://sbml.svn.sourceforge.net/sbml/?rev=15322&view=rev
Author: fbergmann
Date: 2012-01-26 20:36:16 +0000 (Thu, 26 Jan 2012)
Log Message:
-----------
- add the compare line numbers program to SVN in case we ever want to repeat that test
Added Paths:
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trunk/libsbml/dev/utilities/comparelinenumbers/
trunk/libsbml/dev/utilities/comparelinenumbers/LibSBMLLineNumbers.cs
trunk/libsbml/dev/utilities/comparelinenumbers/README.txt
Added: trunk/libsbml/dev/utilities/comparelinenumbers/LibSBMLLineNumbers.cs
===================================================================
--- trunk/libsbml/dev/utilities/comparelinenumbers/LibSBMLLineNumbers.cs (rev 0)
+++ trunk/libsbml/dev/utilities/comparelinenumbers/LibSBMLLineNumbers.cs 2012-01-26 20:36:16 UTC (rev 15322)
@@ -0,0 +1,385 @@
+using System;
+using System.Collections.Generic;
+using System.IO;
+using System.Linq;
+using System.Text;
+using libsbmlcs;
+
+namespace LibSBMLLineNumbers
+{
+ class Program
+ {
+ public static TextWriter Writer { get; set; }
+
+ public static string XMLParser
+ {
+ get
+ {
+ try
+ {
+ // we really ought to have a better way to detect the parser!
+ var stream = new XMLInputStream("<sbml/>", false, "expat", null);
+ if (!stream.isError())
+ return "expat";
+ stream = new XMLInputStream("<sbml/>", false, "libxml", null);
+ if (!stream.isError())
+ return "libxml";
+ stream = new XMLInputStream("<sbml/>", false, "xerces", null);
+ if (!stream.isError())
+ return "xerces-c";
+
+ }
+ catch
+ {
+
+ }
+ return "unknown";
+ }
+ }
+ private static string GetLine(string sbml, long line)
+ {
+ var lines = sbml.Split('\n');
+ if (line-1 < lines.Length)
+ return lines[line - 1];
+ return "invalid line";
+ }
+ private static void PrintLineNumbers(int level, int version, SBMLDocument doc, string message)
+ {
+ //doc.checkInternalConsistency();
+ var sbml = libsbml.writeSBMLToString(doc);
+ var doc2 = libsbml.readSBMLFromString(sbml);
+ doc2.checkConsistency();
+ for (int i = 0; i < doc2.getNumErrors(); i++)
+ {
+ var current = doc2.getError(i);
+ if (current.getSeverity() == libsbml.LIBSBML_SEV_ERROR ||
+ current.getSeverity() == libsbml.LIBSBML_SEV_FATAL)
+ {
+ if (current.getErrorId() == 10103)
+ continue;
+
+ Writer.WriteLine("{0}, {1}, {2}, {3}, {4}, {5}, {6}, {7}, {8}",
+ XMLParser,
+ level,
+ version,
+ message,
+ current.getLine(),
+ current.getColumn(),
+ current.getErrorId(),
+ current.getShortMessage(),
+ GetLine(sbml, current.getLine()));
+ }
+ }
+
+ //libsbml.writeSBMLToFile(doc, string.Format("{0}-l{1}v{2}.xml", message, level, version));
+
+ }
+ private static void TestCompartment(int level, int version)
+ {
+ var doc = new SBMLDocument(level, version);
+ var model = doc.createModel();
+ var comp = model.createCompartment();
+
+ PrintLineNumbers(level,
+ version,
+ doc, "Compartment");
+ }
+ private static void TestCompartmentType(int level, int version)
+ {
+ var doc = new SBMLDocument(level, version);
+ var model = doc.createModel();
+ var comp = model.createCompartmentType();
+
+ PrintLineNumbers(level,
+ version,
+ doc, "CompartmentType");
+ }
+ private static void TestSpecies(int level, int version)
+ {
+ var doc = new SBMLDocument(level, version);
+ var model = doc.createModel();
+ var element = model.createSpecies();
+
+ PrintLineNumbers(level,
+ version,
+ doc, "Species");
+ }
+ private static void TestSpeciesType(int level, int version)
+ {
+ var doc = new SBMLDocument(level, version);
+ var model = doc.createModel();
+ var element = model.createSpeciesType();
+
+ PrintLineNumbers(level,
+ version,
+ doc, "SpeciesType");
+ }
+ private static void TestFunctionDefinition(int level, int version)
+ {
+ var doc = new SBMLDocument(level, version);
+ var model = doc.createModel();
+ var element = model.createFunctionDefinition();
+
+ PrintLineNumbers(level,
+ version,
+ doc, "FunctionDefiniton");
+ }
+ private static void TestParameter(int level, int version)
+ {
+ var doc = new SBMLDocument(level, version);
+ var model = doc.createModel();
+ var element = model.createParameter();
+
+ PrintLineNumbers(level,
+ version,
+ doc, "Parameter");
+ }
+ private static void TestAlgebraicRule(int level, int version)
+ {
+ var doc = new SBMLDocument(level, version);
+ var model = doc.createModel();
+ var element = model.createAlgebraicRule();
+
+ PrintLineNumbers(level,
+ version,
+ doc, "AlgebraicRule");
+ }
+ private static void TestAssignmentRule(int level, int version)
+ {
+ var doc = new SBMLDocument(level, version);
+ var model = doc.createModel();
+ var element = model.createAssignmentRule();
+
+ PrintLineNumbers(level,
+ version,
+ doc, "AssignmentRule");
+ }
+ private static void TestRateRule(int level, int version)
+ {
+ var doc = new SBMLDocument(level, version);
+ var model = doc.createModel();
+ var element = model.createRateRule();
+
+ PrintLineNumbers(level,
+ version,
+ doc, "RateRule");
+ }
+ private static void TestReaction(int level, int version)
+ {
+ var doc = new SBMLDocument(level, version);
+ var model = doc.createModel();
+ var element = model.createReaction();
+
+ PrintLineNumbers(level,
+ version,
+ doc, "Reaction");
+ }
+ private static void TestKineticLaw(int level, int version)
+ {
+ var doc = new SBMLDocument(level, version);
+ var model = doc.createModel();
+ var reaction= model.createReaction();
+
+ reaction.initDefaults();
+ reaction.createKineticLaw();
+
+ PrintLineNumbers(level,
+ version,
+ doc, "KineticLaw");
+ }
+ private static void TestLocalParameter(int level, int version)
+ {
+ var doc = new SBMLDocument(level, version);
+ var model = doc.createModel();
+ var reaction = model.createReaction();
+
+ reaction.initDefaults();
+ var law = reaction.createKineticLaw();
+ law.createParameter();
+
+ PrintLineNumbers(level,
+ version,
+ doc, "LocalParameter");
+ }
+ private static void TestEvent(int level, int version)
+ {
+ var doc = new SBMLDocument(level, version);
+ var model = doc.createModel();
+ var element = model.createEvent();
+
+ PrintLineNumbers(level,
+ version,
+ doc, "Event");
+ }
+ private static void TestEventAssignment(int level, int version)
+ {
+ var doc = new SBMLDocument(level, version);
+ var model = doc.createModel();
+ var element = model.createEvent();
+ if (element == null) return;
+ element.createEventAssignment();
+
+ PrintLineNumbers(level,
+ version,
+ doc, "EventAssignment");
+ }
+ private static void TestTrigger(int level, int version)
+ {
+ var doc = new SBMLDocument(level, version);
+ var model = doc.createModel();
+ var element = model.createEvent();
+ if (element == null) return;
+ element.createTrigger();
+
+ PrintLineNumbers(level,
+ version,
+ doc, "Trigger");
+ }
+ private static void TestDelay(int level, int version)
+ {
+ var doc = new SBMLDocument(level, version);
+ var model = doc.createModel();
+ var element = model.createEvent();
+ if (element == null) return;
+ element.createDelay();
+
+ PrintLineNumbers(level,
+ version,
+ doc, "Delay");
+ }
+ private static void TestPriority(int level, int version)
+ {
+ var doc = new SBMLDocument(level, version);
+ var model = doc.createModel();
+ var element = model.createEvent();
+ if (element == null) return;
+ element.createPriority();
+
+ PrintLineNumbers(level,
+ version,
+ doc, "Priority");
+ }
+ private static void TestConstraint(int level, int version)
+ {
+ var doc = new SBMLDocument(level, version);
+ var model = doc.createModel();
+ var element = model.createConstraint();
+
+ PrintLineNumbers(level,
+ version,
+ doc, "Constraint");
+ }
+ private static void TestInitialAssignment(int level, int version)
+ {
+ var doc = new SBMLDocument(level, version);
+ var model = doc.createModel();
+ var element = model.createInitialAssignment();
+
+ PrintLineNumbers(level,
+ version,
+ doc, "InitialAssignment");
+ }
+ private static void TestSpeciesReference(int level, int version)
+ {
+ var doc = new SBMLDocument(level, version);
+ var model = doc.createModel();
+ var reaction = model.createReaction();
+
+ reaction.initDefaults();
+ var sr = reaction.createReactant();
+
+
+ PrintLineNumbers(level,
+ version,
+ doc, "SpeciesReference");
+ }
+ private static void TestStoichiometryMath(int level, int version)
+ {
+ var doc = new SBMLDocument(level, version);
+ var model = doc.createModel();
+ var reaction = model.createReaction();
+
+ reaction.initDefaults();
+ var sr = reaction.createReactant();
+ sr.createStoichiometryMath();
+
+ PrintLineNumbers(level,
+ version,
+ doc, "StoichiometryMath");
+ }
+ private static void TestUnit(int level, int version)
+ {
+ var doc = new SBMLDocument(level, version);
+ var model = doc.createModel();
+ var element = model.createUnitDefinition();
+ var element1 = model.createUnit();
+
+ PrintLineNumbers(level,
+ version,
+ doc, "Unit");
+ }
+ private static void TestUnitDefinition(int level, int version)
+ {
+ var doc = new SBMLDocument(level, version);
+ var model = doc.createModel();
+ var element = model.createUnitDefinition();
+
+ PrintLineNumbers(level,
+ version,
+ doc, "UnitDefinition");
+ }
+ private static void TestSBMLLevelVersion(int level, int version)
+ {
+ TestCompartment(level, version);
+ TestCompartmentType(level, version);
+ TestSpecies(level, version);
+ TestSpeciesType(level, version);
+ TestFunctionDefinition(level, version);
+ TestParameter(level, version);
+ TestAlgebraicRule(level, version);
+ TestAssignmentRule(level, version);
+ TestRateRule(level, version);
+ TestReaction(level, version);
+ TestKineticLaw(level, version);
+ TestLocalParameter(level, version);
+ TestEvent(level, version);
+ TestEventAssignment(level, version);
+ TestTrigger(level, version);
+ TestDelay(level, version);
+ TestPriority(level, version);
+ TestConstraint(level, version);
+ TestInitialAssignment(level, version);
+ TestSpeciesReference(level, version);
+ TestStoichiometryMath(level, version);
+ TestUnit(level, version);
+ TestUnitDefinition(level, version);
+ }
+
+ static void Main(string[] args)
+ {
+ Writer = Console.Out;
+
+ var versions = new List<int[]> { new [] {1, 1}
+ , new [] {1, 1}
+ , new [] {1, 2}
+ , new [] {2, 1}
+ , new [] {2, 2}
+ , new [] {2, 3}
+ , new [] {2, 4}
+ , new [] {3, 1}
+ };
+
+ Writer.WriteLine("Testing libSBML {0} xml parser: {1}", libsbml.getLibSBMLDottedVersion(), XMLParser);
+ Writer.WriteLine();
+ Writer.WriteLine("Parser, Level, Version, Element, Line, Column, ErrorId, ShortMessage, XML Snippet");
+
+ foreach (var item in versions)
+ {
+ TestSBMLLevelVersion(item[0], item[1]);
+ }
+
+ //Console.ReadKey();
+
+ }
+ }
+}
Added: trunk/libsbml/dev/utilities/comparelinenumbers/README.txt
===================================================================
--- trunk/libsbml/dev/utilities/comparelinenumbers/README.txt (rev 0)
+++ trunk/libsbml/dev/utilities/comparelinenumbers/README.txt 2012-01-26 20:36:16 UTC (rev 15322)
@@ -0,0 +1,10 @@
+The LibSBMLLineNumbers.cs file goes constructs invalid SBMLDocuments containing
+all the different SBML components. Next it validates the document printing the
+errors and error locations in CSV format.
+
+Once compiled the program can simply run with the libsbml C# bindings using the
+different XML parsers which enables us to compare the error location reported by
+each parser.
+
+See also pivotal:
+https://www.pivotaltracker.com/story/show/23689513
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